diff --git a/_reader/RNAseqWorkshop.pdf b/_reader/RNAseqWorkshop.pdf index fc61e85050fa86d9901987a8072d30b921d723df..cb58970bab7087441631133a445aa8af56be043d 100644 Binary files a/_reader/RNAseqWorkshop.pdf and b/_reader/RNAseqWorkshop.pdf differ diff --git a/_reader/sections/00_section_arc.tex b/_reader/sections/00_section_arc.tex index b78a4c9d9f474acb87281a8fbe26d77e93bebbf3..7ccf058fc13a1642990885936e6c3effc9985b13 100644 --- a/_reader/sections/00_section_arc.tex +++ b/_reader/sections/00_section_arc.tex @@ -94,7 +94,7 @@ run: \begin{lstlisting} docker run -it --name rnalive -p 8889:8889 --mount \ - type=bind,source="$(pwd)"/rnaseq-workshop,target=/home/ZIM-gast/rnaseq-workshop \ + type=bind,source="$(pwd)"/rnaseq-workshop,target=/home/zim-gast/rnaseq-workshop \ rnaseq:latest \end{lstlisting} diff --git a/_reader/sections/01_section_linux.tex b/_reader/sections/01_section_linux.tex index be7e146824582c1ad2b575e683d0e8ac529abc69..a8d6ac681566b2f447f5a4b1e5cf2d01eda3bf55 100644 --- a/_reader/sections/01_section_linux.tex +++ b/_reader/sections/01_section_linux.tex @@ -397,8 +397,8 @@ this. \begin{lstlisting} docker image load -i </path/to/>rstudio_docker.tar docker run --rm -p 8787:8787 -e PASSWORD=rstudio --mount \ - type=bind,source=${PWD}/rnaseq-workshop,target=/home/ZIM-gast/rnaseq-workshop \ - rstudiotest + type=bind,source=${PWD}/rnaseq-workshop,target=/home/zim-gast/rnaseq-workshop \ + rstudio \end{lstlisting} \begin{itemize} \item on the \emph{host} machine go to the browser and enter 'localhost:8787' @@ -418,7 +418,7 @@ Within Rstudio, the first thing we'll want to do is navigate to the usual directory. \begin{lstlisting} -setwd('/home/ZIM-gast/rnaseq-workshop/') +setwd('/home/zim-gast/rnaseq-workshop/') \end{lstlisting} \subsubsection{basics in R and Rstudio} diff --git a/workflows/docker/instructions.md b/workflows/docker/instructions.md index 6c398b395599f51bd92edbb0bdfa3539773e7ade..63f8de37333e8013b71a83300a855672eed91ef2 100644 --- a/workflows/docker/instructions.md +++ b/workflows/docker/instructions.md @@ -16,7 +16,7 @@ It is in no-way a good practice example. Do this from the parent directory of the 'rnaseq-workshop' repository, so that the mounted folder contains the repository -`sudo docker run -it --name rnalive --rm --mount type=bind,source="$(pwd)"/rnaseq-workshop,target=/home/ZIM-gast/rnaseq-workshop rnaseq:latest` +`sudo docker run -it --name rnalive --rm --mount type=bind,source="$(pwd)"/rnaseq-workshop,target=/home/zim-gast/rnaseq-workshop rnaseq:latest` > Note difference to user instructions with `--rm`, so you don't end up with > tons of copies of the same container, nor naming conflicts.